jupyter-analysis-tools 1.3.2__py3-none-any.whl → 1.4.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- jupyter_analysis_tools/__init__.py +4 -5
- jupyter_analysis_tools/plotting.py +25 -0
- jupyter_analysis_tools/readdata.py +31 -8
- jupyter_analysis_tools/utils.py +40 -3
- {jupyter_analysis_tools-1.3.2.dist-info → jupyter_analysis_tools-1.4.1.dist-info}/METADATA +149 -96
- jupyter_analysis_tools-1.4.1.dist-info/RECORD +16 -0
- jupyter_analysis_tools-1.3.2.dist-info/RECORD +0 -16
- {jupyter_analysis_tools-1.3.2.dist-info → jupyter_analysis_tools-1.4.1.dist-info}/WHEEL +0 -0
- {jupyter_analysis_tools-1.3.2.dist-info → jupyter_analysis_tools-1.4.1.dist-info}/licenses/AUTHORS.rst +0 -0
- {jupyter_analysis_tools-1.3.2.dist-info → jupyter_analysis_tools-1.4.1.dist-info}/licenses/LICENSE +0 -0
- {jupyter_analysis_tools-1.3.2.dist-info → jupyter_analysis_tools-1.4.1.dist-info}/top_level.txt +0 -0
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# -*- coding: utf-8 -*-
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# __init__.py
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__version__ = "1.
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__version__ = "1.4.1"
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from .binning import reBin
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from .git import checkRepo, isNBstripoutActivated, isNBstripoutInstalled, isRepo
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from .
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from .readdata import readdata
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from .
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from .utils import setLocaleUTF8
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from .plotting import createFigure, plotPDH
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from .readdata import readdata, readPDH, readPDHmeta, readSSF, readSSFZ
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from .utils import naturalKey, setLocaleUTF8
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from .widgets import PathSelector, showBoolStatus
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setLocaleUTF8()
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@@ -4,6 +4,8 @@
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import matplotlib
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import matplotlib.pyplot as plt
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from .readdata import readPDH
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try:
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# increase the limit for the warning to pop up
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matplotlib.rcParams["figure.max_open_warning"] = 50
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def lineWidth():
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return plt.rcParams["lines.linewidth"]
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def plotPDH(filename, label, **kwargs):
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"""Plot a given .PDH file with the given label (shown in legend) using pandas and readPDH()."""
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q_range = kwargs.pop("q_range", None)
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print_filename = kwargs.pop("print_filename", True) # default value from readdata()
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df, _ = readPDH(filename, q_range=q_range, print_filename=print_filename)
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df["e"] = df["e"].clip(lower=0)
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defaults = dict(
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yerr="e",
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logx=True,
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logy=True,
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label=label,
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grid=True,
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figsize=(10, 5),
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xlabel=r"$q$ (nm$^{{-1}}$)",
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ylabel="Intensity",
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ecolor="lightgray",
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)
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for k, v in defaults.items():
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if k not in kwargs:
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kwargs[k] = v
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df.plot("q", "I", **kwargs)
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# -*- coding: utf-8 -*-
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# readdata.py
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import tempfile
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import warnings
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import xml.etree.ElementTree as et
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import zipfile
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from pathlib import Path
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import pandas as pd
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return df, filename
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readPDH = readdata
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def convertValue(val):
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val = val.strip()
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try:
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@@ -146,25 +151,43 @@ def xmlPDHToDict(root):
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return result
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def readPDHmeta(
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def readPDHmeta(pathPDH):
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"""Reads the XML metadata at the end of a .PDH file to a Python dict."""
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pathPDH = Path(pathPDH)
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if pathPDH.suffix.lower() != ".pdh":
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warnings.warn("readPDHmeta() supports .pdh files only!")
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return # for PDH files
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lines = ""
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with open(
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with open(pathPDH) as fd:
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lines = fd.readlines()
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nrows = int(lines[2].split()[0])
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xml = "".join(lines[nrows + 5 :])
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return xmlPDHToDict(et.fromstring(xml))
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def readSSF(
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def readSSF(pathSSF):
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"""Reads the SAXSquant session file *pathSSF* (.SSF) to a Python dict."""
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pathSSF = Path(pathSSF)
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if pathSSF.suffix.lower() != ".ssf":
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warnings.warn("readSession() supports .ssf files only!")
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return # for PDH files
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data = ""
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with open(
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with open(pathSSF, encoding="utf-8-sig") as fd:
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data = fd.read()
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return xmlPDHToDict(et.fromstring(data))
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def readSSFZ(pathSSFZ):
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"""Extracts and reads the SAXSquant session file (.SSF) to a Python dict.
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The .SSF is embedded in the .SSFZ provided by *pathSSFZ*."""
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assert pathSSFZ.is_file()
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# unpack the SSFZ to a temporary dir
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data = None
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with tempfile.TemporaryDirectory() as tempdir:
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with zipfile.ZipFile(pathSSFZ, "r") as zipfd:
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zipfd.extractall(tempdir)
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# read the session metadata from the extracted SSF file
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pathSSF = next(Path(tempdir).glob("*.ssf"))
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assert pathSSF.is_file()
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data = readSSF(pathSSF)
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return data
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jupyter_analysis_tools/utils.py
CHANGED
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import locale
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import os
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import platform
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import re
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import subprocess
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import sys
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from pathlib import Path
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[row[1:3] for row in rows if row[1].endswith(":") and row[2].startswith("\\\\")]
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)
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return rows
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else: # Linux (tested) or macOS (untested)
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if cmdOutput is None:
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proc = subprocess.run(["mount"], capture_output=True, text=True)
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cmdOutput = proc.stdout
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def parse(line):
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# position of last opening parenthesis, start of options list
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lastParen = list(i for i, c in enumerate(line) if "(" == c)[-1]
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line = line[:lastParen].strip()
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spaces = list(i for i, c in enumerate(line) if " " == c)
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fstype = line[spaces[-1] :].strip() # last remaining word is the filesystem type
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line = line[: spaces[-2]].strip() # strip the 'type' indicator as well
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sepIdx = line.find(" on /") # separates destination from mount point
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dest = line[:sepIdx].strip()
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mountpoint = line[sepIdx + 4 :].strip()
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yield (mountpoint, dest, fstype)
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return {
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mp: dst
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for line in cmdOutput.strip().splitlines()
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for (mp, dst, fstype) in parse(line)
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if fstype in ("nfs", "cifs", "sshfs", "afs", "ext4")
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}
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return {}
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def makeNetworkdriveAbsolute(filepath, cmdOutput: str = None):
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"""Replaces the drive letter of the given path by the respective network path, if possible."""
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if
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if filepath.drive.startswith(r"\\"):
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return # it's a UNC path already
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if isWindows():
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drivemap = networkdriveMapping(cmdOutput=cmdOutput)
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prefix = drivemap.get(filepath.drive, None)
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if prefix is not None:
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filepath = Path(prefix).joinpath(*filepath.parts[1:])
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drivemap = networkdriveMapping(cmdOutput=cmdOutput)
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# search for the mountpoint, starting with the longest, most specific, first
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for mp, target in sorted(drivemap.items(), key=lambda tup: len(tup[0]), reverse=True):
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if filepath.is_relative_to(mp):
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return Path(target).joinpath(filepath.relative_to(mp))
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["7z", "x", fn],
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Metadata-Version: 2.4
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Name: jupyter-analysis-tools
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Version: 1.
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Version: 1.4.1
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Summary: Yet another Python library with helpers and utilities for data analysis and processing.
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Author-email: Ingo Breßler <ingo.bressler@bam.de>, "Brian R. Pauw" <brian.pauw@bam.de>
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License-Expression: MIT
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Classifier: Topic :: Scientific/Engineering
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Classifier: Intended Audience :: Developers
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Classifier: Intended Audience :: Science/Research
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: numpy
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#
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Yet another Python library with helpers and utilities for data analysis and processing.
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# Jupyter Analysis Tools (v1.4.1)
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[](https://pypi.org/project/jupyter-analysis-tools)
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[](https://github.com/BAMresearch/jupyter-analysis-tools/compare/v1.4.1...main)
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[](https://en.wikipedia.org/wiki/MIT_license)
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[](https://pypi.org/project/jupyter-analysis-tools)
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[](https://pypi.org/project/jupyter-analysis-tools#files)
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[](https://github.com/BAMresearch/jupyter-analysis-tools/actions/workflows/ci-cd.yml)
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[](https://BAMresearch.github.io/jupyter-analysis-tools/coverage-report/)
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Yet another Python library with helpers and utilities for data analysis and processing.
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## Installation
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pip install jupyter-analysis-tools
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## Development
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### Testing
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See which tests are available (arguments after `--` get passed to *pytest* which runs the tests):
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tox -e py -- --co
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### Package Version
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Get the next version number and how the GIT history would be interpreted for that:
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This prints its interpretation of the commits in detail. Make sure to supply the `--print`
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argument to not raise the version number which is done automatically by the *release* job
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of the GitHub Action Workflows.
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### Project template
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# CHANGELOG
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## v1.4.1 (2025-08-01)
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### Bug fixes
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* **utils**: networkdriveMapping() for Linux, with tests ([`3f4deeb`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/3f4deebdf57cc9162121c26d5d7d8484f1f0ec63))
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### Testing
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* **utils**: remove debug output, should work now ([`1117c89`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/1117c89d4206c6880373e3b8765dff6e48d3ccd5))
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* **Changelog&Readme**: updated by template ([`ab2efa8`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/ab2efa808b7c96b9bf63fdb333c09f070c19b754))
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* **readme**: note on reapplying project template ([`a8d0176`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/a8d01764645c9996bb1e2af60ba6c2d1ee33363a))
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* **readme**: .rst version not needed anymore ([`a59e9a8`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/a59e9a81b7165c67f6c02906d0266d93f7deaca3))
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* **Utils**: naturalKey() can be used as sort key for natural file sorting ([`a60f186`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/a60f1864a87c435a165cebc885f0b55de52db796))
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* feat: readSSFZ() convenience function ([`c3e882b`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/c3e882bc1d26be578b41c60c1f6b0df94cd83025))
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* **Project**: let the template generate supported python versions ([`8acfa6d`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/8acfa6d337ea4b8b92f8ea623e961af1be9a0f17))
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* **coverage**: revert config regression for coverage merging ([`dffe265`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/dffe265af9779253a698f241e725d0ea03ea2979))
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* **readme**: additional fix for readme.md ([`795046f`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/795046f73ada0ae85b4eb050c8453cc096c43122))
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* **readme**: in markdown format for combining with changelog ([`eb6b904`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/eb6b904136697ddc2427369a605058e464d49351))
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* **readme**: use markdown format to allow combining with changelog on PyPI ([`395b2c0`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/395b2c0c72232e9109ca50c5b84a7fce2d423df4))
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* **utils**: satisfy flake8 ([`2e3dc36`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/2e3dc36ef21e60f4fe7b8caea567411cc69967c0))
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* **semantic-release**: replace .cookiecutterrc by .copier-answers.yml ([`2030c88`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/2030c88dfb0ca69ac332380e33b3baed9cb6cf44))
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* **coverage**: coverage-report fix ([`1bd26b7`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/1bd26b71abcb090ef32cb2fbdd05b978bce5144c))
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* **GitHub Workflows**: remove templates, rendered by *copier update* ([`8a637a5`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/8a637a5b34df4a3ec6a4e8cae97a9d3e24ad2e5c))
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* **GitHub Workflow**: publish depends on all other job to be successful ([`efc1f22`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/efc1f223aa2da882d43b27406a2f20113c2c8879))
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* **Template**: latest GitHub Workflow templates applied ([`7d87906`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/7d87906c852cb2b57704c45db0b19c7a1ae513a2))
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* **coverage**: fix path name matching rules ([`37bd2d9`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/37bd2d93a8fe10a3355feee6779f45bd9161a88b))
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* **Copyright years**: update ([`cee35e6`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/cee35e6fe92ae27575bd7fb4a7a2638cd1c931b2))
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* **Contributions**: Authors update ([`dd5a5c4`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/dd5a5c4d81732821057bcc200f462159cffa760b))
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* **Project**: GitHub Workflow templates fixed ([`b346b28`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/b346b282332f0f7f81b724509a4004e6a69d7791))
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* **Project**: GitHub Workflow templates updated ([`235c4d9`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/235c4d9c53997fdf4c08913361fb57167939cd7c))
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* **Project**: switching to copier for project template with update mechanism ([`0d3064b`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/0d3064b8cef45667b0964aab248b583424946207))
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* **utils.extract7z**: informative info message ([`80d2f71`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/80d2f7134992d59f0bfd7f5e7bc27772f77cd452))
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* **coverage**: fix coverage artifact name for multiple matrix.os ([`f471599`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/f471599b8c86e29fd20b78f7cbd9291c3a6dd98a))
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* **testing**: test on Windows as well ([`4a83c39`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/4a83c3924bcb820ef0728af40b86a0f6622dfef2))
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* **utils.makeNetworkdriveAbsolute**: new routines for translating a windows drive letter mount to its network location ([`823a6bf`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/823a6bfe126829381bc14d34578f342f4b9d3e8f))
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* **pyproject**: revert specify readme+changelog document types ([`1baa762`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/1baa762d441fe0a1b7b663b9d0589de857277426))
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* **pyproject**: specify readme+changelog document types to render overview on pypi correctly ([`6e4d1e5`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/6e4d1e56640b604f971ddca8dabd8d1aff5c9bf1))
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* **ghpages**: make sure .nojekyll exists after purging old html docs ([`4847845`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/4847845cc06884b6e589b26897e83411d649ef4d))
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* **readme**: trigger new version after style changes ([`8b2b5e9`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/8b2b5e93c0f24ae59afaa764abdc508e994946b4))
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* **__init__**: imports format ([`6f07790`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/6f07790a04e43736b1c0fbce0eac54d0b661a7cf))
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* **utils**: satisfy flake8 ([`9657474`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/9657474e94a4d9887c4a6b653e0ffa403e666d02))
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* **readdata**: satisfy flake8 ([`36bf6e8`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/36bf6e8be67a2ebd345c5557c2352710bcebed82))
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* **workflow**: publish only if the docs are good ([`a663ed3`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/a663ed3d1fd87079a4fd7cf419132a129280a562))
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* **utils**: fix imports ([`ddd5369`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/ddd5369b8037f583c6900aea25522a56126c9d32))
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* **readPDHmeta**: routine for reading metadata part from .PDH and .SSF files ([`ea6a1d5`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/ea6a1d554f3763fc05022ae8e4e8909f0993cd43))
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* **readdata**: path separator depends on platform ([`1b2866f`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/1b2866f13307c2cf2dedc59f36d7372442ddbfd8))
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* **readdata**: testdata files and testing, using pathlib instead of old os.path ([`aeacfa4`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/aeacfa4a949d7293f2cd3ce5e3004fddf20ecc02))
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* **utils**: appendToPATH() using pathlib, verifed test included ([`35f37fc`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/35f37fc19cdcf4b575dc0525400f3c0212bb0faf))
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* **packaging**: add required dependency packages to project config ([`43076e2`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/43076e2fd27e511545d8f1ec12752435cf5153c6))
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* **semver**: allow message tag *enh* for enhancements ([`0810b4f`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/0810b4fd58e1b2383313496b657a800078260c83))
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* **Changelog**: omit *empty* versions without relevant changes ([`87b7f23`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/87b7f2360c5224a6570f8687e8008e2293b81ddb))
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* **readme**: license link ([`f98f736`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/f98f7362dd0278210894f138dd7646c8bc92cc9f))
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* **Package**: cookiecutterrc updated ([`7b29a17`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/7b29a1764f972379086abb51194604423c9714f2))
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* **readme**: using test.pypi.org links ([`240e58c`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/240e58c87ef0cf0dc3d195f237a09c8e8a717e75))
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* **Package**: update project description ([`704a0b5`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/704a0b50a727ef36f685d27ce068103ffa60ca99))
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* **Documentation**: doctest format in *distrib* ([`5942972`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/59429724fd41e62c7717fa185e7f5c5c1e5b50d9))
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* **readme**: updated links and badges ([`2e0329d`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/2e0329d510bb5c090d093818c0536993c6292a8a))
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* **config**: clean up version definition ([`c18c67f`](https://github.com/BAMresearch/jupyter-analysis-tools/commit/c18c67fae8852f2acdd79ffe3bcb89aa5821c797))
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jupyter_analysis_tools-1.3.2.dist-info/licenses/LICENSE,sha256=jRVl3hmCq0Qv1wifm-EelEKhFWecdoWdhcxSte4a1_c,1125
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13
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jupyter_analysis_tools-1.3.2.dist-info/METADATA,sha256=m7O2CREPyjxd2aYi4n-vz4o13d4bzsOmfFQUNTRiTBY,41321
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14
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jupyter_analysis_tools-1.3.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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15
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jupyter_analysis_tools-1.3.2.dist-info/top_level.txt,sha256=ei_0x-BF85FLoJ_h67ySwDFowtqus_gI4_0GR466PEU,23
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16
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jupyter_analysis_tools-1.3.2.dist-info/RECORD,,
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File without changes
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File without changes
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{jupyter_analysis_tools-1.3.2.dist-info → jupyter_analysis_tools-1.4.1.dist-info}/licenses/LICENSE
RENAMED
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File without changes
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{jupyter_analysis_tools-1.3.2.dist-info → jupyter_analysis_tools-1.4.1.dist-info}/top_level.txt
RENAMED
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File without changes
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